Karen Eilbeck

Karen Eilbeck, MSc, PhD, FACMI

Languages spoken: English

Academic Information

Departments Primary - Biomedical Informatics , Adjunct - Human Genetics

Dr. Karen Eilbeck earned both her M.Sc. degree in Bioinformatics and her Ph.D. in Biochemistry at the University of Manchester in England. She did postdoctoral training in the Department of Computer Science at the University of Manchester. She is a Professor in the University of Utah’s Biomedical Informatics Department. Prior to moving to Utah, she was a scientist at Celera Genomics in Maryland, and at the Berkeley Drosophila Genome Project at U.C. Berkeley.

Dr. Eilbeck maintains an active lab where the main focus is knowledge representation for genomic data. She has mentored successful Ph.D. & MS students and post docs who have gone on to academic, government, and industry positions. Her expertise is in managing and accessing biological data in order to better understand diseases. Her research involves the annotation of biological sequences, in particular genome sequences. Genomic annotation is the process of adding further knowledge to the raw sequence data, such as the location of genes, the functions of the gene products, and the positions of known mutations. Her group maintains the Sequence Ontology, an open-source project for organizing and naming the parts of genomic sequence and the relationships between these parts. This project has unified the vocabulary used to annotate genomes, enabling computational exploration of data from many sources. It forms the terminology used by many genome software programs and model organism communities. She continues to work with the GA4GH standards development organization to build interoperability around biological data. Her group worked closely with the ClinGen Initiative where they developed ClinVar Miner – a tool for clinical genetics professionals to better understand ClinVar submissions.

More information about Dr. Eilbeck can be found at: https://eilbecklab.chpc.utah.edu/updates/

Google Scholar: http://scholar.google.com/citations?hl=en&user=ccf6djEAAAAJ

Research Statement

Quality control of genomic annotations; Management and analysis of personal genomics data; Ontology development to structure biological, genomic and phenotypic data

Education History

Undergraduate University of Salford
 BSc
Graduate Training University of Manchester
 MSc
Doctoral Training University of Manchester
 PhD
Postdoctoral Training University of Manchester, Department of Computer Science, Genome Information Management System
 Postdoctoral Training

Selected Publications

Journal Article

  1. Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M (2014). Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet, 94(4), 599-610.
  2. Moore B, Fan G, Eilbeck (2010). SOBA: sequence ontology bioinformatics analysis. Nucleic acids research, 38(Web Server issue), W161-4.
  3. Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Bofill-De Ros X, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano (2020). Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics (Oxford, England), 36(3), 698-703.
  4. Eilbeck K, Moore B, Holt C, Yandell (2009). Quantitative measures for the management and comparison of annotated genomes. BMC bioinformatics, 10, 67.
  5. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner (2005). The Sequence Ontology: a tool for the unification of genome annotations. Genome biology, 6(5), R44.
  6. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck (2010). A standard variation file format for human genome sequences. Genome biology, 11(8), R88.
  7. Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, Dechene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzy Ski P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, Macarthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, Deluca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovre I L, Palanda I A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, Gonzalez-Lamuno D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies D (2014). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome biology, 15(3), R53.
  8. Ruiz-Schultz N, Sant D, Norcross S, Dansithong W, Hart K, Asay B, Little J, Chung K, Oakeson KF, Young EL, Eilbeck K, Rohrwasser (2021). Methods and feasibility study for exome sequencing as a universal second-tier test in newborn screening. Genetics in medicine, 23(4), 767-776.
  9. Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides (2020). Redefining fundamental concepts of transcription initiation in bacteria. Nature reviews. Genetics, 21(11), 699-714.
  10. Mungall CJ, Batchelor C, Eilbeck (2011). Evolution of the Sequence Ontology terms and relationships. Journal of biomedical informatics, 44(1), 87-93.
  11. Welch BM, Eilbeck K, Del Fiol G, Meyer LJ, Kawamoto (2014). Technical desiderata for the integration of genomic data with clinical decision support. Journal of biomedical informatics, 51, 3-7.
  12. Watkins M, Rynearson S, Henrie A, Eilbeck (2020). Implementing the VMC Specification to Reduce Ambiguity in Genomic Variant Representation. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2019, 1226-1235.
  13. Lario R, Hasley S, White SA, Eilbeck K, Soley R, Huff S, Kawamoto (2021). Utilization of BPM+ Health for the Representation of Clinical Knowledge: A Framework for the Expression and Assessment of Clinical Practice Guidelines (CPG) Utilizing Existing and Emerging Object Management Group (OMG) Standards. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2020, 687-696.
  14. Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan (2014). OMIT: dynamic, semi-automated ontology development for the microRNA domain. PloS one, 9(7), e100855.
  15. Duncan J, Eilbeck K, Narus SP, Clyde S, Thornton S, Staes (2015). Building an Ontology for Identity Resolution in Healthcare and Public Health. Online journal of public health informatics, 7(2), e219.
  16. Watkins M, Eilbeck (2020). FHIR Lab Reports: using SMART on FHIR and CDS Hooks to increase the clinical utility of pharmacogenomic laboratory test results. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2020, 683-692.
  17. Watkins M, Au A, Vuong T, Wallis H, Hart K, Rohrwasser A, Eilbeck (2021). ResultsMyWay: combining Fast Healthcare Interoperability Resources (FHIR), Clinical Quality Language (CQL), and informational resources to create a newborn screening application. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2021, 615-623.
  18. Brandon M. Welch , Salvador Rodriguez Loya , Karen Eilbeck and Kensaku Kawamoto (2014). A Proposed Clinical Decision Support Architecture Capable of Supporting Whole Genome Sequence Information. Journal of personalized medicine, 4(2), 176-199.
  19. Sant DW, Sinclair M, Mungall CJ, Schulz S, Zerbino D, Lovering RC, Logie C, Eilbeck (2021). Sequence Ontology terminology for gene regulation. Biochimica et biophysica acta. Gene regulatory mechanisms, 1864(10), 194745.
  20. Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Udara Liyanage I, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O'Connor BD, Oesterle S, Ogishima S, Wang VO, Paglione LAD, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney (2021). GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell genomics, 1(2),
  21. Lario R, Kawamoto K, Sottara D, Eilbeck K, Huff S, Del Fiol G, Soley R, Middleton (2023). A method for structuring complex clinical knowledge and its representational formalisms to support composite knowledge interoperability in healthcare. Journal of biomedical informatics, 137, 104251.
  22. Kiser AC, Eilbeck K, Ferraro JP, Skarda DE, Samore MH, Bucher (2022). Standard Vocabularies to Improve Machine Learning Model Transferability With Electronic Health Record Data: Retrospective Cohort Study Using Health Care-Associated Infection. JMIR medical informatics, 10(8), e39057.
  23. Conway M, Vuong TT, Hart K, Rohrwasser A, Eilbeck (2022). Pain points in parents' interactions with newborn screening systems: a qualitative study. BMC pediatrics, 22(1), 167.
  24. Weso'owski S, Lemmon G, Hernandez EJ, Henrie A, Miller TA, Weyhrauch D, Puchalski MD, Bray BE, Shah RU, Deshmukh VG, Delaney R, Yostl HJ, Eilbeck K, Tristani-Firouzi M, Yandell (2022). An explainable artificial intelligence approach for predicting cardiovascular outcomes using electronic health records. PLOS digital health, 1(1),
  25. Kiser AC, Eilbeck K, Bucher B (2023). Developing an LSTM Model to Identify Surgical Site Infections using Electronic Healthcare Records. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2023, 330-339.
  26. Engelsma T, Anders C, Oudbier SJ, Eilbeck K, Knaup P, Peute LW, Ganzinger (2023). Proposing a Novel Hybrid Short-Term Exchange Program in Biomedical and Health Informatics Education. Studies in health technology and informatics, 302, 498-499.
  27. Watkins MT, Kohlmann WK, Berry TS, Sama NR, Koptiuch C, Rynearson SG, Eilbeck K (2023). LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2022, 1145-1152.
  28. Han S, DiBlasi E, Monson ET, Shabalin A, Ferris E, Chen D, Fraser A, Yu Z, Staley M, Callor WB, Christensen ED, Crockett DK, Li QS, Willour V, Bakian AV, Keeshin B, Docherty AR, Eilbeck K, Coon (2023). Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes. Molecular psychiatry, 28(9), 3909-3919.
  29. Lario R, Soley R, White S, Butler J, Del Fiol G, Eilbeck K, Huff S, Kawamoto (2024). The Business Process Management for Healthcare (BPM+ Health) Consortium: motivation, methodology, and deliverables for enabling clinical knowledge interoperability (CKI). Journal of the American Medical Informatics Association, 31(4), 797-808.
  30. Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware J (2023). Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genetics in medicine, 26(2), 101029.
  31. Kiser AC, Schliep KC, Hernandez EJ, Peterson CM, Yandell M, Eilbeck (2024). An artificial intelligence approach for investigating multifactorial pain-related features of endometriosis. PloS one, 19(2), e0297998.
  32. Han S, Cho SA, Choi W, Eilbeck K, Coon H, Nho K, Lee (2025). Interaction of genetic variants and methylation in transcript-level expression regulation in Alzheimer's disease by multi-omics data analysis. BMC genomics, 26(1), 170.
  33. Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, van Sant D, Stark Z, Whiffin N, Rehm HL, Ware J (2023). Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms.
  34. Kiser AC, Hemmert R, Myrer R, Bucher BT, Eilbeck K, Varner M, Stanford JB, Peterson CM, Pollack AZ, Farland LV, Schliep K (2025). Validation of administrative health data for the identification of endometriosis diagnosis. Human reproduction (Oxford, England), 40(2), 289-295.
  35. Valdez LA, Hernandez EJ, Matthews O, Mulvey M, Crandall H, Eilbeck (2025). Probabilistic Graphical Models for Evaluating the Utility of Data-Driven ICD Code Categories in Pediatric Sepsis. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2024, 1149-1158.
  36. Taber P, Baysinger J, Daniels S, Diaz-Kincaid N, Gaviglio A, Ginter J, Held PK, Reeves E, Sack V, Weaver J, Eilbeck (2025). Participatory Workflow Analysis of Newborn Genetic Screening (NBS) to Support Tools for Improved Follow-Up: Comparing the Use Case of Hemoglobinopathy Traits Across U.S. States. International journal of neonatal screening, 11(2),
  37. Olsen BB, Tristani-Firouzi M, Eilbeck K, Yandell M, Hernandez E (2025). Quantifying lifetime risk for 1,401 infectious diseases across the diabetes spectrum using a Bayesian approach.
  38. Christensen E, Gauchel C, Valdez L, Rayguru C, Sholokhova K, Upadhyay U, Dewi SRK, Aigner M, Phariss M, Holleboom M, Groenevelt C, Eilbeck K, Abdul S (2025). Student Perspectives from the International Partnership for Health Informatics Education (IPHIE) 2024 Master Class. Studies in health technology and informatics, 329, 2038-2039.

Letter

  1. Duncan J, Narus SP, Clyde S, Eilbeck K, Thornton S, Staes (2015). Birth of identity: understanding changes to birth certificates and their value for identity resolution. Journal of the American Medical Informatics Association, 22(e1), e120-9.